Magnesium in PDB 1mcz: Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate
Enzymatic activity of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate
All present enzymatic activity of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate:
4.1.1.7;
Protein crystallography data
The structure of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate, PDB code: 1mcz
was solved by
E.S.Polovnikova,
A.K.Bera,
M.S.Hasson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
30.00 /
2.80
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
134.800,
209.600,
163.400,
90.00,
97.10,
90.00
|
|
R / Rfree (%)
|
20 /
22
|
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
24;
Binding sites:
The binding sites of Magnesium atom in the Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate
(pdb code 1mcz). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the
Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate, PDB code: 1mcz:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 24 in 1mcz
Go back to
Magnesium Binding Sites List in 1mcz
Magnesium binding site 1 out
of 24 in the Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg529
b:1.8
occ:1.00
|
O
|
A:HOH547
|
2.1
|
1.8
|
1.0
|
|
O
|
A:THR457
|
2.3
|
12.4
|
1.0
|
|
OD1
|
A:ASN455
|
2.3
|
17.4
|
1.0
|
|
OD1
|
A:ASP428
|
2.3
|
20.3
|
1.0
|
|
O12
|
A:TDP533
|
2.7
|
20.0
|
1.0
|
|
O21
|
A:TDP533
|
2.8
|
21.1
|
1.0
|
|
O11
|
A:TDP533
|
2.9
|
18.2
|
1.0
|
|
CG
|
A:ASN455
|
3.1
|
16.4
|
1.0
|
|
ND2
|
A:ASN455
|
3.3
|
17.7
|
1.0
|
|
P1
|
A:TDP533
|
3.4
|
18.2
|
1.0
|
|
P2
|
A:TDP533
|
3.5
|
17.8
|
1.0
|
|
C
|
A:THR457
|
3.5
|
12.7
|
1.0
|
|
CG
|
A:ASP428
|
3.5
|
20.9
|
1.0
|
|
N
|
A:THR457
|
3.9
|
13.7
|
1.0
|
|
OD2
|
A:ASP428
|
4.1
|
18.6
|
1.0
|
|
N
|
A:GLY459
|
4.1
|
15.1
|
1.0
|
|
N
|
A:ASP428
|
4.2
|
18.7
|
1.0
|
|
O5G
|
A:TDP533
|
4.2
|
17.2
|
1.0
|
|
O23
|
A:TDP533
|
4.3
|
19.0
|
1.0
|
|
CA
|
A:THR457
|
4.3
|
12.7
|
1.0
|
|
O
|
A:MET453
|
4.3
|
17.3
|
1.0
|
|
N
|
A:ASN455
|
4.4
|
15.6
|
1.0
|
|
N
|
A:GLY429
|
4.4
|
17.8
|
1.0
|
|
O
|
A:HOH571
|
4.4
|
6.7
|
1.0
|
|
CB
|
A:ASN455
|
4.5
|
15.7
|
1.0
|
|
N
|
A:TYR458
|
4.5
|
13.4
|
1.0
|
|
O22
|
A:TDP533
|
4.6
|
18.6
|
1.0
|
|
CA
|
A:TYR458
|
4.6
|
14.3
|
1.0
|
|
O13
|
A:TDP533
|
4.6
|
19.0
|
1.0
|
|
CG2
|
A:THR457
|
4.7
|
10.8
|
1.0
|
|
N
|
A:GLY456
|
4.7
|
16.6
|
1.0
|
|
CB
|
A:ASP428
|
4.7
|
20.2
|
1.0
|
|
CA
|
A:ASN455
|
4.8
|
15.8
|
1.0
|
|
C
|
A:ASN455
|
4.8
|
16.5
|
1.0
|
|
CA
|
A:GLY427
|
4.8
|
17.6
|
1.0
|
|
C
|
A:GLY427
|
4.9
|
18.2
|
1.0
|
|
CA
|
A:ASP428
|
4.9
|
18.9
|
1.0
|
|
C
|
A:TYR458
|
4.9
|
15.7
|
1.0
|
|
CA
|
A:GLY459
|
4.9
|
15.2
|
1.0
|
|
Magnesium binding site 2 out
of 24 in 1mcz
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Magnesium Binding Sites List in 1mcz
Magnesium binding site 2 out
of 24 in the Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg530
b:25.4
occ:1.00
|
O
|
A:LEU118
|
2.5
|
12.2
|
1.0
|
|
O
|
A:ARG120
|
2.5
|
14.2
|
1.0
|
|
O
|
B:LEU118
|
2.5
|
14.6
|
1.0
|
|
O
|
B:ARG120
|
2.5
|
12.7
|
1.0
|
|
O
|
A:ASN117
|
2.6
|
12.9
|
1.0
|
|
O
|
B:ASN117
|
2.8
|
12.1
|
1.0
|
|
C
|
A:LEU118
|
3.2
|
12.5
|
1.0
|
|
C
|
B:LEU118
|
3.3
|
13.7
|
1.0
|
|
C
|
A:ARG120
|
3.6
|
13.3
|
1.0
|
|
CA
|
A:LEU118
|
3.6
|
12.5
|
1.0
|
|
C
|
B:ARG120
|
3.7
|
13.3
|
1.0
|
|
C
|
A:ASN117
|
3.7
|
12.7
|
1.0
|
|
CA
|
B:LEU118
|
3.8
|
13.7
|
1.0
|
|
N
|
A:ARG120
|
3.8
|
13.2
|
1.0
|
|
C
|
B:ASN117
|
3.9
|
13.4
|
1.0
|
|
N
|
B:ARG120
|
3.9
|
13.6
|
1.0
|
|
N
|
A:LEU118
|
4.2
|
12.8
|
1.0
|
|
CA
|
A:ARG120
|
4.2
|
12.9
|
1.0
|
|
C
|
A:PRO119
|
4.2
|
13.3
|
1.0
|
|
N
|
A:PRO119
|
4.2
|
12.4
|
1.0
|
|
N
|
B:LEU118
|
4.3
|
14.4
|
1.0
|
|
CA
|
B:ARG120
|
4.3
|
13.0
|
1.0
|
|
C
|
B:PRO119
|
4.3
|
13.7
|
1.0
|
|
CE
|
B:MET79
|
4.3
|
11.9
|
0.5
|
|
N
|
B:PRO119
|
4.4
|
13.3
|
1.0
|
|
CE
|
A:MET79
|
4.4
|
11.6
|
0.5
|
|
CB
|
A:ARG120
|
4.5
|
12.5
|
1.0
|
|
CA
|
A:PRO119
|
4.6
|
12.6
|
1.0
|
|
CA
|
B:PRO119
|
4.7
|
13.4
|
1.0
|
|
CB
|
B:ARG120
|
4.7
|
12.5
|
1.0
|
|
N
|
A:PRO121
|
4.7
|
13.4
|
1.0
|
|
N
|
B:PRO121
|
4.8
|
13.0
|
1.0
|
|
O
|
A:PRO119
|
4.8
|
13.9
|
1.0
|
|
CD
|
A:PRO121
|
4.9
|
12.7
|
1.0
|
|
O
|
B:PRO119
|
5.0
|
13.6
|
1.0
|
|
CD
|
B:PRO121
|
5.0
|
11.1
|
1.0
|
|
CD1
|
A:LEU118
|
5.0
|
13.1
|
1.0
|
|
CD1
|
B:LEU118
|
5.0
|
11.8
|
1.0
|
|
CA
|
A:ASN117
|
5.0
|
12.8
|
1.0
|
|
Magnesium binding site 3 out
of 24 in 1mcz
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Magnesium Binding Sites List in 1mcz
Magnesium binding site 3 out
of 24 in the Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg529
b:1.8
occ:1.00
|
OD1
|
B:ASP428
|
2.3
|
19.6
|
1.0
|
|
O
|
B:HOH551
|
2.3
|
4.8
|
1.0
|
|
O
|
B:THR457
|
2.4
|
17.9
|
1.0
|
|
OD1
|
B:ASN455
|
2.4
|
17.1
|
1.0
|
|
O12
|
B:TDP533
|
2.6
|
16.6
|
1.0
|
|
O21
|
B:TDP533
|
2.8
|
17.8
|
1.0
|
|
O11
|
B:TDP533
|
2.8
|
16.9
|
1.0
|
|
CG
|
B:ASN455
|
3.2
|
17.5
|
1.0
|
|
P1
|
B:TDP533
|
3.3
|
15.9
|
1.0
|
|
ND2
|
B:ASN455
|
3.4
|
17.4
|
1.0
|
|
CG
|
B:ASP428
|
3.5
|
18.8
|
1.0
|
|
P2
|
B:TDP533
|
3.5
|
15.2
|
1.0
|
|
C
|
B:THR457
|
3.6
|
17.1
|
1.0
|
|
N
|
B:THR457
|
4.0
|
17.9
|
1.0
|
|
OD2
|
B:ASP428
|
4.0
|
19.1
|
1.0
|
|
N
|
B:ASP428
|
4.1
|
18.8
|
1.0
|
|
O
|
B:HOH572
|
4.1
|
21.2
|
1.0
|
|
O5G
|
B:TDP533
|
4.2
|
17.1
|
1.0
|
|
N
|
B:GLY459
|
4.2
|
17.5
|
1.0
|
|
O
|
B:MET453
|
4.3
|
18.9
|
1.0
|
|
O23
|
B:TDP533
|
4.3
|
17.0
|
1.0
|
|
N
|
B:GLY429
|
4.3
|
18.4
|
1.0
|
|
N
|
B:ASN455
|
4.4
|
17.3
|
1.0
|
|
CA
|
B:THR457
|
4.4
|
16.9
|
1.0
|
|
CB
|
B:ASN455
|
4.5
|
16.2
|
1.0
|
|
O13
|
B:TDP533
|
4.5
|
18.0
|
1.0
|
|
N
|
B:TYR458
|
4.5
|
16.8
|
1.0
|
|
O22
|
B:TDP533
|
4.6
|
15.9
|
1.0
|
|
CB
|
B:ASP428
|
4.6
|
17.9
|
1.0
|
|
CA
|
B:TYR458
|
4.7
|
16.6
|
1.0
|
|
CA
|
B:GLY427
|
4.7
|
18.9
|
1.0
|
|
C
|
B:GLY427
|
4.7
|
19.4
|
1.0
|
|
N
|
B:GLY456
|
4.7
|
17.7
|
1.0
|
|
CA
|
B:ASP428
|
4.8
|
18.4
|
1.0
|
|
CG2
|
B:THR457
|
4.8
|
13.8
|
1.0
|
|
CA
|
B:ASN455
|
4.8
|
16.6
|
1.0
|
|
C
|
B:ASN455
|
4.9
|
17.3
|
1.0
|
|
C
|
B:TYR458
|
5.0
|
17.1
|
1.0
|
|
Magnesium binding site 4 out
of 24 in 1mcz
Go back to
Magnesium Binding Sites List in 1mcz
Magnesium binding site 4 out
of 24 in the Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg529
b:1.8
occ:1.00
|
OD1
|
C:ASP428
|
2.4
|
19.3
|
1.0
|
|
O
|
C:THR457
|
2.4
|
17.7
|
1.0
|
|
O
|
C:HOH550
|
2.4
|
1.8
|
1.0
|
|
OD1
|
C:ASN455
|
2.4
|
21.5
|
1.0
|
|
O21
|
C:TDP533
|
2.7
|
19.1
|
1.0
|
|
O12
|
C:TDP533
|
2.7
|
19.8
|
1.0
|
|
O11
|
C:TDP533
|
2.7
|
17.8
|
1.0
|
|
CG
|
C:ASN455
|
3.1
|
20.9
|
1.0
|
|
P1
|
C:TDP533
|
3.3
|
18.1
|
1.0
|
|
ND2
|
C:ASN455
|
3.3
|
20.3
|
1.0
|
|
P2
|
C:TDP533
|
3.3
|
15.2
|
1.0
|
|
CG
|
C:ASP428
|
3.6
|
19.5
|
1.0
|
|
C
|
C:THR457
|
3.6
|
16.6
|
1.0
|
|
N
|
C:THR457
|
4.1
|
15.8
|
1.0
|
|
N
|
C:GLY459
|
4.1
|
16.9
|
1.0
|
|
O5G
|
C:TDP533
|
4.1
|
18.6
|
1.0
|
|
N
|
C:ASP428
|
4.1
|
16.9
|
1.0
|
|
OD2
|
C:ASP428
|
4.1
|
20.3
|
1.0
|
|
O23
|
C:TDP533
|
4.2
|
17.5
|
1.0
|
|
O
|
C:HOH572
|
4.3
|
26.6
|
1.0
|
|
O
|
C:MET453
|
4.3
|
17.5
|
1.0
|
|
N
|
C:GLY429
|
4.4
|
16.6
|
1.0
|
|
N
|
C:ASN455
|
4.4
|
17.1
|
1.0
|
|
CA
|
C:THR457
|
4.4
|
15.3
|
1.0
|
|
O22
|
C:TDP533
|
4.4
|
16.4
|
1.0
|
|
O13
|
C:TDP533
|
4.5
|
19.4
|
1.0
|
|
CB
|
C:ASN455
|
4.5
|
18.5
|
1.0
|
|
N
|
C:TYR458
|
4.6
|
16.8
|
1.0
|
|
CA
|
C:TYR458
|
4.7
|
17.4
|
1.0
|
|
CA
|
C:GLY427
|
4.7
|
15.7
|
1.0
|
|
CB
|
C:ASP428
|
4.7
|
17.0
|
1.0
|
|
CG2
|
C:THR457
|
4.8
|
12.0
|
1.0
|
|
C
|
C:GLY427
|
4.8
|
16.1
|
1.0
|
|
N
|
C:GLY456
|
4.8
|
15.9
|
1.0
|
|
CA
|
C:ASN455
|
4.9
|
17.7
|
1.0
|
|
CA
|
C:ASP428
|
4.9
|
16.9
|
1.0
|
|
C
|
C:ASN455
|
4.9
|
16.7
|
1.0
|
|
CA
|
C:GLY459
|
4.9
|
17.5
|
1.0
|
|
C
|
C:TYR458
|
5.0
|
17.2
|
1.0
|
|
Magnesium binding site 5 out
of 24 in 1mcz
Go back to
Magnesium Binding Sites List in 1mcz
Magnesium binding site 5 out
of 24 in the Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg529
b:1.8
occ:1.00
|
O
|
D:HOH553
|
2.2
|
6.8
|
1.0
|
|
O
|
D:THR457
|
2.3
|
17.0
|
1.0
|
|
OD1
|
D:ASP428
|
2.5
|
18.8
|
1.0
|
|
OD1
|
D:ASN455
|
2.5
|
19.2
|
1.0
|
|
O12
|
D:TDP533
|
2.6
|
18.4
|
1.0
|
|
O21
|
D:TDP533
|
2.6
|
21.0
|
1.0
|
|
O11
|
D:TDP533
|
2.6
|
19.3
|
1.0
|
|
P1
|
D:TDP533
|
3.1
|
17.1
|
1.0
|
|
P2
|
D:TDP533
|
3.3
|
20.1
|
1.0
|
|
CG
|
D:ASN455
|
3.3
|
18.6
|
1.0
|
|
ND2
|
D:ASN455
|
3.4
|
18.9
|
1.0
|
|
C
|
D:THR457
|
3.5
|
16.3
|
1.0
|
|
CG
|
D:ASP428
|
3.7
|
17.9
|
1.0
|
|
N
|
D:GLY459
|
3.9
|
15.1
|
1.0
|
|
O5G
|
D:TDP533
|
3.9
|
16.8
|
1.0
|
|
O23
|
D:TDP533
|
4.0
|
19.9
|
1.0
|
|
O
|
D:HOH575
|
4.0
|
4.5
|
1.0
|
|
N
|
D:THR457
|
4.1
|
17.3
|
1.0
|
|
N
|
D:ASP428
|
4.2
|
16.2
|
1.0
|
|
OD2
|
D:ASP428
|
4.3
|
17.9
|
1.0
|
|
N
|
D:GLY429
|
4.4
|
15.1
|
1.0
|
|
CA
|
D:THR457
|
4.4
|
16.4
|
1.0
|
|
N
|
D:TYR458
|
4.4
|
16.1
|
1.0
|
|
O22
|
D:TDP533
|
4.4
|
19.9
|
1.0
|
|
O13
|
D:TDP533
|
4.4
|
17.4
|
1.0
|
|
CA
|
D:TYR458
|
4.4
|
15.1
|
1.0
|
|
O
|
D:MET453
|
4.5
|
14.7
|
1.0
|
|
N
|
D:ASN455
|
4.6
|
17.1
|
1.0
|
|
CB
|
D:ASN455
|
4.7
|
17.6
|
1.0
|
|
C
|
D:TYR458
|
4.7
|
15.2
|
1.0
|
|
CG2
|
D:THR457
|
4.7
|
14.0
|
1.0
|
|
CA
|
D:GLY427
|
4.8
|
16.7
|
1.0
|
|
CA
|
D:GLY459
|
4.8
|
15.1
|
1.0
|
|
C
|
D:GLY427
|
4.8
|
16.5
|
1.0
|
|
CB
|
D:ASP428
|
4.9
|
15.9
|
1.0
|
|
CA
|
D:ASP428
|
4.9
|
15.6
|
1.0
|
|
N
|
D:GLY456
|
5.0
|
17.5
|
1.0
|
|
Magnesium binding site 6 out
of 24 in 1mcz
Go back to
Magnesium Binding Sites List in 1mcz
Magnesium binding site 6 out
of 24 in the Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg530
b:17.5
occ:1.00
|
O
|
D:ARG120
|
2.4
|
12.6
|
1.0
|
|
O
|
C:LEU118
|
2.5
|
11.1
|
1.0
|
|
O
|
D:LEU118
|
2.6
|
14.4
|
1.0
|
|
O
|
C:ASN117
|
2.6
|
11.6
|
1.0
|
|
O
|
C:ARG120
|
2.7
|
14.7
|
1.0
|
|
O
|
D:ASN117
|
2.7
|
12.3
|
1.0
|
|
C
|
C:LEU118
|
3.3
|
12.3
|
1.0
|
|
C
|
D:LEU118
|
3.3
|
14.0
|
1.0
|
|
C
|
D:ARG120
|
3.5
|
13.1
|
1.0
|
|
CA
|
C:LEU118
|
3.6
|
11.1
|
1.0
|
|
C
|
C:ASN117
|
3.7
|
12.5
|
1.0
|
|
N
|
D:ARG120
|
3.8
|
13.0
|
1.0
|
|
CA
|
D:LEU118
|
3.8
|
13.4
|
1.0
|
|
C
|
D:ASN117
|
3.8
|
12.7
|
1.0
|
|
C
|
C:ARG120
|
3.8
|
12.9
|
1.0
|
|
N
|
C:ARG120
|
3.9
|
13.1
|
1.0
|
|
CA
|
D:ARG120
|
4.1
|
12.9
|
1.0
|
|
N
|
C:LEU118
|
4.1
|
11.8
|
1.0
|
|
C
|
D:PRO119
|
4.2
|
13.0
|
1.0
|
|
N
|
D:LEU118
|
4.3
|
12.8
|
1.0
|
|
N
|
D:PRO119
|
4.3
|
13.7
|
1.0
|
|
CA
|
C:ARG120
|
4.3
|
12.7
|
1.0
|
|
N
|
C:PRO119
|
4.3
|
13.3
|
1.0
|
|
C
|
C:PRO119
|
4.4
|
14.9
|
1.0
|
|
CB
|
D:ARG120
|
4.4
|
11.0
|
1.0
|
|
CE
|
D:MET79
|
4.5
|
11.4
|
0.5
|
|
CE
|
C:MET79
|
4.6
|
11.3
|
0.5
|
|
N
|
D:PRO121
|
4.6
|
13.4
|
1.0
|
|
CB
|
C:ARG120
|
4.6
|
11.6
|
1.0
|
|
CA
|
D:PRO119
|
4.6
|
13.0
|
1.0
|
|
CA
|
C:PRO119
|
4.7
|
14.0
|
1.0
|
|
CD
|
D:PRO121
|
4.8
|
12.7
|
1.0
|
|
O
|
D:PRO119
|
4.8
|
12.7
|
1.0
|
|
CD1
|
C:LEU118
|
4.9
|
10.3
|
1.0
|
|
N
|
C:PRO121
|
4.9
|
12.3
|
1.0
|
|
CA
|
C:ASN117
|
5.0
|
13.2
|
1.0
|
|
CB
|
C:LEU118
|
5.0
|
9.3
|
1.0
|
|
Magnesium binding site 7 out
of 24 in 1mcz
Go back to
Magnesium Binding Sites List in 1mcz
Magnesium binding site 7 out
of 24 in the Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg529
b:1.8
occ:1.00
|
OD1
|
E:ASP428
|
2.2
|
21.6
|
1.0
|
|
O
|
E:HOH546
|
2.3
|
8.4
|
1.0
|
|
O
|
E:THR457
|
2.4
|
18.3
|
1.0
|
|
OD1
|
E:ASN455
|
2.5
|
16.1
|
1.0
|
|
O12
|
E:TDP533
|
2.5
|
19.8
|
1.0
|
|
O11
|
E:TDP533
|
2.8
|
19.1
|
1.0
|
|
O21
|
E:TDP533
|
2.8
|
20.4
|
1.0
|
|
P1
|
E:TDP533
|
3.2
|
17.7
|
1.0
|
|
CG
|
E:ASN455
|
3.3
|
16.9
|
1.0
|
|
CG
|
E:ASP428
|
3.4
|
21.6
|
1.0
|
|
P2
|
E:TDP533
|
3.5
|
17.6
|
1.0
|
|
ND2
|
E:ASN455
|
3.5
|
18.7
|
1.0
|
|
C
|
E:THR457
|
3.6
|
17.1
|
1.0
|
|
OD2
|
E:ASP428
|
4.0
|
21.7
|
1.0
|
|
N
|
E:ASP428
|
4.0
|
19.4
|
1.0
|
|
N
|
E:THR457
|
4.0
|
17.8
|
1.0
|
|
O5G
|
E:TDP533
|
4.1
|
17.9
|
1.0
|
|
N
|
E:GLY429
|
4.2
|
17.5
|
1.0
|
|
N
|
E:GLY459
|
4.2
|
16.4
|
1.0
|
|
O23
|
E:TDP533
|
4.3
|
19.3
|
1.0
|
|
O
|
E:MET453
|
4.3
|
17.1
|
1.0
|
|
CA
|
E:THR457
|
4.4
|
16.6
|
1.0
|
|
O
|
E:HOH568
|
4.4
|
1.8
|
1.0
|
|
N
|
E:ASN455
|
4.4
|
16.5
|
1.0
|
|
O13
|
E:TDP533
|
4.5
|
15.8
|
1.0
|
|
N
|
E:TYR458
|
4.5
|
16.2
|
1.0
|
|
CB
|
E:ASP428
|
4.6
|
20.0
|
1.0
|
|
O22
|
E:TDP533
|
4.6
|
20.1
|
1.0
|
|
CB
|
E:ASN455
|
4.6
|
16.6
|
1.0
|
|
CA
|
E:GLY427
|
4.6
|
18.4
|
1.0
|
|
CA
|
E:TYR458
|
4.6
|
15.9
|
1.0
|
|
C
|
E:GLY427
|
4.7
|
19.5
|
1.0
|
|
CA
|
E:ASP428
|
4.7
|
18.8
|
1.0
|
|
N
|
E:GLY456
|
4.8
|
16.4
|
1.0
|
|
CG2
|
E:THR457
|
4.8
|
14.1
|
1.0
|
|
CA
|
E:ASN455
|
4.9
|
16.3
|
1.0
|
|
C
|
E:ASP428
|
4.9
|
17.8
|
1.0
|
|
C
|
E:ASN455
|
5.0
|
16.0
|
1.0
|
|
C
|
E:TYR458
|
5.0
|
15.9
|
1.0
|
|
Magnesium binding site 8 out
of 24 in 1mcz
Go back to
Magnesium Binding Sites List in 1mcz
Magnesium binding site 8 out
of 24 in the Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg530
b:31.8
occ:1.00
|
O
|
F:ASN117
|
2.1
|
14.1
|
1.0
|
|
O
|
F:LEU118
|
2.2
|
16.1
|
1.0
|
|
O
|
E:ARG120
|
2.3
|
14.9
|
1.0
|
|
C
|
F:LEU118
|
2.7
|
14.3
|
1.0
|
|
CA
|
F:LEU118
|
2.9
|
13.1
|
1.0
|
|
O
|
F:ARG120
|
3.0
|
15.7
|
1.0
|
|
C
|
F:ASN117
|
3.1
|
13.6
|
1.0
|
|
O
|
E:LEU118
|
3.1
|
13.7
|
1.0
|
|
O
|
E:ASN117
|
3.4
|
13.9
|
1.0
|
|
N
|
F:LEU118
|
3.4
|
13.3
|
1.0
|
|
C
|
E:ARG120
|
3.5
|
13.9
|
1.0
|
|
N
|
F:ARG120
|
3.7
|
13.4
|
1.0
|
|
N
|
F:PRO119
|
3.8
|
15.0
|
1.0
|
|
C
|
E:LEU118
|
4.0
|
13.2
|
1.0
|
|
C
|
F:ARG120
|
4.0
|
14.9
|
1.0
|
|
N
|
E:ARG120
|
4.2
|
11.9
|
1.0
|
|
C
|
F:PRO119
|
4.2
|
14.3
|
1.0
|
|
CB
|
F:LEU118
|
4.3
|
12.7
|
1.0
|
|
CA
|
F:ARG120
|
4.3
|
14.2
|
1.0
|
|
CA
|
E:ARG120
|
4.3
|
13.6
|
1.0
|
|
CA
|
F:PRO119
|
4.3
|
14.7
|
1.0
|
|
N
|
E:PRO121
|
4.4
|
14.0
|
1.0
|
|
CD
|
E:PRO121
|
4.4
|
13.8
|
1.0
|
|
CA
|
F:ASN117
|
4.4
|
13.4
|
1.0
|
|
CD1
|
F:LEU118
|
4.5
|
10.0
|
1.0
|
|
C
|
E:ASN117
|
4.5
|
12.8
|
1.0
|
|
CA
|
E:LEU118
|
4.5
|
13.1
|
1.0
|
|
CB
|
F:ARG120
|
4.5
|
11.2
|
1.0
|
|
CE
|
F:MET79
|
4.5
|
11.0
|
0.5
|
|
CE
|
E:MET79
|
4.6
|
14.4
|
0.5
|
|
C
|
E:PRO119
|
4.6
|
12.7
|
1.0
|
|
CB
|
E:ARG120
|
4.7
|
12.9
|
1.0
|
|
CG
|
F:LEU118
|
4.8
|
12.8
|
1.0
|
|
CB
|
F:ASN117
|
4.8
|
12.6
|
1.0
|
|
N
|
E:PRO119
|
4.9
|
14.1
|
1.0
|
|
O
|
F:PRO119
|
5.0
|
15.6
|
1.0
|
|
CD
|
F:PRO119
|
5.0
|
16.2
|
1.0
|
|
Magnesium binding site 9 out
of 24 in 1mcz
Go back to
Magnesium Binding Sites List in 1mcz
Magnesium binding site 9 out
of 24 in the Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg529
b:1.8
occ:1.00
|
O
|
F:THR457
|
2.2
|
16.9
|
1.0
|
|
O
|
F:HOH554
|
2.3
|
1.8
|
1.0
|
|
OD1
|
F:ASN455
|
2.4
|
19.8
|
1.0
|
|
O21
|
F:TDP533
|
2.5
|
21.6
|
1.0
|
|
OD1
|
F:ASP428
|
2.6
|
21.1
|
1.0
|
|
O11
|
F:TDP533
|
2.7
|
22.0
|
1.0
|
|
O12
|
F:TDP533
|
2.7
|
22.1
|
1.0
|
|
CG
|
F:ASN455
|
3.2
|
19.6
|
1.0
|
|
P1
|
F:TDP533
|
3.2
|
21.8
|
1.0
|
|
P2
|
F:TDP533
|
3.2
|
22.9
|
1.0
|
|
ND2
|
F:ASN455
|
3.3
|
19.8
|
1.0
|
|
C
|
F:THR457
|
3.4
|
16.8
|
1.0
|
|
CG
|
F:ASP428
|
3.7
|
20.8
|
1.0
|
|
N
|
F:GLY459
|
3.8
|
18.0
|
1.0
|
|
O5G
|
F:TDP533
|
4.0
|
20.0
|
1.0
|
|
O23
|
F:TDP533
|
4.0
|
23.1
|
1.0
|
|
N
|
F:THR457
|
4.0
|
17.6
|
1.0
|
|
OD2
|
F:ASP428
|
4.3
|
18.2
|
1.0
|
|
CA
|
F:THR457
|
4.3
|
16.6
|
1.0
|
|
N
|
F:TYR458
|
4.3
|
17.1
|
1.0
|
|
N
|
F:ASP428
|
4.3
|
18.3
|
1.0
|
|
O
|
F:HOH576
|
4.4
|
26.9
|
1.0
|
|
CA
|
F:TYR458
|
4.4
|
17.3
|
1.0
|
|
O22
|
F:TDP533
|
4.4
|
20.5
|
1.0
|
|
N
|
F:GLY429
|
4.5
|
18.2
|
1.0
|
|
O13
|
F:TDP533
|
4.5
|
21.7
|
1.0
|
|
O
|
F:MET453
|
4.6
|
17.8
|
1.0
|
|
CG2
|
F:THR457
|
4.6
|
14.1
|
1.0
|
|
CB
|
F:ASN455
|
4.6
|
18.1
|
1.0
|
|
N
|
F:ASN455
|
4.6
|
17.2
|
1.0
|
|
C
|
F:TYR458
|
4.7
|
18.2
|
1.0
|
|
CA
|
F:GLY459
|
4.7
|
18.6
|
1.0
|
|
CA
|
F:GLY427
|
4.9
|
17.9
|
1.0
|
|
N
|
F:GLY456
|
4.9
|
18.1
|
1.0
|
|
CB
|
F:ASP428
|
4.9
|
19.9
|
1.0
|
|
C
|
F:GLY427
|
5.0
|
18.2
|
1.0
|
|
CA
|
F:ASN455
|
5.0
|
17.5
|
1.0
|
|
C
|
F:ASN455
|
5.0
|
18.2
|
1.0
|
|
Magnesium binding site 10 out
of 24 in 1mcz
Go back to
Magnesium Binding Sites List in 1mcz
Magnesium binding site 10 out
of 24 in the Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed with An Inhibitor, R-Mandelate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg529
b:1.8
occ:1.00
|
O
|
G:HOH550
|
2.2
|
6.5
|
1.0
|
|
O
|
G:THR457
|
2.3
|
14.6
|
1.0
|
|
OD1
|
G:ASN455
|
2.4
|
17.6
|
1.0
|
|
OD1
|
G:ASP428
|
2.4
|
19.8
|
1.0
|
|
O21
|
G:TDP533
|
2.7
|
18.3
|
1.0
|
|
O12
|
G:TDP533
|
2.7
|
19.5
|
1.0
|
|
O11
|
G:TDP533
|
2.8
|
19.2
|
1.0
|
|
CG
|
G:ASN455
|
3.1
|
19.0
|
1.0
|
|
P1
|
G:TDP533
|
3.3
|
18.1
|
1.0
|
|
ND2
|
G:ASN455
|
3.3
|
19.4
|
1.0
|
|
P2
|
G:TDP533
|
3.4
|
17.5
|
1.0
|
|
C
|
G:THR457
|
3.5
|
14.7
|
1.0
|
|
CG
|
G:ASP428
|
3.6
|
17.7
|
1.0
|
|
N
|
G:THR457
|
4.0
|
14.7
|
1.0
|
|
N
|
G:GLY459
|
4.0
|
16.7
|
1.0
|
|
OD2
|
G:ASP428
|
4.1
|
18.8
|
1.0
|
|
O5G
|
G:TDP533
|
4.1
|
17.9
|
1.0
|
|
O23
|
G:TDP533
|
4.2
|
18.9
|
1.0
|
|
N
|
G:ASP428
|
4.2
|
16.3
|
1.0
|
|
O
|
G:HOH571
|
4.2
|
20.5
|
1.0
|
|
CA
|
G:THR457
|
4.3
|
14.8
|
1.0
|
|
O
|
G:MET453
|
4.4
|
19.5
|
1.0
|
|
N
|
G:GLY429
|
4.4
|
16.1
|
1.0
|
|
N
|
G:ASN455
|
4.4
|
18.0
|
1.0
|
|
N
|
G:TYR458
|
4.5
|
15.7
|
1.0
|
|
CB
|
G:ASN455
|
4.5
|
17.8
|
1.0
|
|
O22
|
G:TDP533
|
4.5
|
16.8
|
1.0
|
|
CA
|
G:TYR458
|
4.6
|
17.0
|
1.0
|
|
O13
|
G:TDP533
|
4.6
|
18.0
|
1.0
|
|
CG2
|
G:THR457
|
4.7
|
13.1
|
1.0
|
|
CB
|
G:ASP428
|
4.8
|
16.7
|
1.0
|
|
CA
|
G:GLY427
|
4.8
|
16.2
|
1.0
|
|
N
|
G:GLY456
|
4.8
|
16.1
|
1.0
|
|
C
|
G:GLY427
|
4.8
|
17.0
|
1.0
|
|
CA
|
G:ASN455
|
4.9
|
17.4
|
1.0
|
|
C
|
G:TYR458
|
4.9
|
16.9
|
1.0
|
|
CA
|
G:GLY459
|
4.9
|
16.4
|
1.0
|
|
C
|
G:ASN455
|
4.9
|
16.3
|
1.0
|
|
CA
|
G:ASP428
|
4.9
|
16.3
|
1.0
|
|
Reference:
E.S.Polovnikova,
M.J.Mcleish,
E.A.Sergienko,
J.T.Burgner,
N.L.Anderson,
A.K.Bera,
F.Jordan,
G.L.Kenyon,
M.S.Hasson.
Structural and Kinetic Analysis of Catalysis By A Thiamin Diphosphate-Dependent Enzyme, Benzoylformate Decarboxylase Biochemistry V. 42 1820 2003.
ISSN: ISSN 0006-2960
PubMed: 12590569
DOI: 10.1021/BI026490K
Page generated: Sun Aug 10 00:50:15 2025
|
